Class: DissociatedCellSample

name: DissociatedCellSample
description: A collection of dissociated cells or nuclei derived from dissociation
  of a tissue sample.
in_subset:
- bican
- library_generation
from_schema: https://identifiers.org/brain-bican/library-generation-schema
exact_mappings:
- NIMP:Dissociated%20Cell%20Sample
is_a: material sample
mixins:
- ProvEntity
slots:
- was_generated_by
- was_derived_from
- name
slot_usage:
  was_generated_by:
    name: was_generated_by
    description: The cell dissociation process from which the dissociated cell sample
      was generated by.
    domain_of:
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryPool
    - DissectionRoiPolygon
    - ProvEntity
    range: CellDissociation
  was_derived_from:
    name: was_derived_from
    description: The input tissue sample(s) from which dissociated cell sample was
      derived from.
    exact_mappings:
    - NIMP:has_parent
    domain_of:
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DigitalAsset
    - ProvEntity
    range: TissueSample
    multivalued: true
  name:
    name: name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: dissociated_cell_sample_local_name
    description: Name of a collection of dissociated cells or nuclei derived from
      dissociation of a tissue sample.
    exact_mappings:
    - NIMP:PD-RQRWHS40
    slot_uri: bican:65e2c7da-9eb4-45b2-8ccb-d69ef9785ee2
    domain_of:
    - Donor
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DissectionRoiPolygon
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - macromolecular machine mixin
    - gene or gene product
    - gene
    - genome
attributes:
  cell_prep_type:
    name: cell_prep_type
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: dissociated_cell_sample_cell_prep_type
    description: 'The type of cell preparation. For example: Cells, Nuclei. This is
      a property of dissociated_cell_sample.'
    in_subset:
    - analysis
    - tracking
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-RELLGO26
    rank: 1000
    slot_uri: bican:baae4ac3-f959-4594-b943-3a82ec19bd34
    alias: dissociated cell sample cell prep type
    domain_of:
    - DissociatedCellSample
    range: dissociated_cell_sample_cell_prep_type
  cell_source_oligo_name:
    name: cell_source_oligo_name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: dissociated_cell_sample_cell_label_barcode
    description: Name of cell source oligo used in cell plexing.  The oligo molecularly
      tags all the cells in the dissociated cell sample and allows separate dissociated
      cell samples to be combined downstream in the barcoded cell sample.  The oligo
      name is associated with a sequence in a lookup table.  This sequence will be
      needed during alignment to associate reads with the parent source dissociated
      cell sample.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-CFCFPS27
    rank: 1000
    slot_uri: bican:184abbaf-baff-4b5f-b51e-dd38de6006af
    alias: dissociated cell oligo tag name
    domain_of:
    - DissociatedCellSample
    - EnrichedCellSample
    range: dissociated_cell_sample_cell_label_barcode

name: DissociatedCellSample
description: A collection of dissociated cells or nuclei derived from dissociation
  of a tissue sample.
in_subset:
- bican
- library_generation
from_schema: https://identifiers.org/brain-bican/library-generation-schema
exact_mappings:
- NIMP:Dissociated%20Cell%20Sample
is_a: material sample
mixins:
- ProvEntity
slot_usage:
  was_generated_by:
    name: was_generated_by
    description: The cell dissociation process from which the dissociated cell sample
      was generated by.
    domain_of:
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryPool
    - DissectionRoiPolygon
    - ProvEntity
    range: CellDissociation
  was_derived_from:
    name: was_derived_from
    description: The input tissue sample(s) from which dissociated cell sample was
      derived from.
    exact_mappings:
    - NIMP:has_parent
    domain_of:
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DigitalAsset
    - ProvEntity
    range: TissueSample
    multivalued: true
  name:
    name: name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: dissociated_cell_sample_local_name
    description: Name of a collection of dissociated cells or nuclei derived from
      dissociation of a tissue sample.
    exact_mappings:
    - NIMP:PD-RQRWHS40
    slot_uri: bican:65e2c7da-9eb4-45b2-8ccb-d69ef9785ee2
    domain_of:
    - Donor
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DissectionRoiPolygon
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - macromolecular machine mixin
    - gene or gene product
    - gene
    - genome
attributes:
  cell_prep_type:
    name: cell_prep_type
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: dissociated_cell_sample_cell_prep_type
    description: 'The type of cell preparation. For example: Cells, Nuclei. This is
      a property of dissociated_cell_sample.'
    in_subset:
    - analysis
    - tracking
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-RELLGO26
    rank: 1000
    slot_uri: bican:baae4ac3-f959-4594-b943-3a82ec19bd34
    alias: dissociated cell sample cell prep type
    owner: DissociatedCellSample
    domain_of:
    - DissociatedCellSample
    range: dissociated_cell_sample_cell_prep_type
  cell_source_oligo_name:
    name: cell_source_oligo_name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: dissociated_cell_sample_cell_label_barcode
    description: Name of cell source oligo used in cell plexing.  The oligo molecularly
      tags all the cells in the dissociated cell sample and allows separate dissociated
      cell samples to be combined downstream in the barcoded cell sample.  The oligo
      name is associated with a sequence in a lookup table.  This sequence will be
      needed during alignment to associate reads with the parent source dissociated
      cell sample.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-CFCFPS27
    rank: 1000
    slot_uri: bican:184abbaf-baff-4b5f-b51e-dd38de6006af
    alias: dissociated cell oligo tag name
    owner: DissociatedCellSample
    domain_of:
    - DissociatedCellSample
    - EnrichedCellSample
    range: dissociated_cell_sample_cell_label_barcode
  was_generated_by:
    name: was_generated_by
    description: The cell dissociation process from which the dissociated cell sample
      was generated by.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    slot_uri: prov:wasGeneratedBy
    alias: was_generated_by
    owner: DissociatedCellSample
    domain_of:
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryPool
    - DissectionRoiPolygon
    - ProvEntity
    range: CellDissociation
  was_derived_from:
    name: was_derived_from
    description: The input tissue sample(s) from which dissociated cell sample was
      derived from.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:has_parent
    rank: 1000
    slot_uri: prov:wasDerivedFrom
    alias: was_derived_from
    owner: DissociatedCellSample
    domain_of:
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DigitalAsset
    - ProvEntity
    range: TissueSample
    multivalued: true
  name:
    name: name
    definition_uri: https://w3id.org/biolink/vocab/name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: dissociated_cell_sample_local_name
    description: Name of a collection of dissociated cells or nuclei derived from
      dissociation of a tissue sample.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-RQRWHS40
    rank: 1000
    domain: entity
    slot_uri: bican:65e2c7da-9eb4-45b2-8ccb-d69ef9785ee2
    alias: name
    owner: DissociatedCellSample
    domain_of:
    - Donor
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DissectionRoiPolygon
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - macromolecular machine mixin
    - gene or gene product
    - gene
    - genome
    range: label type
  id:
    name: id
    definition_uri: https://w3id.org/biolink/vocab/id
    description: A unique identifier for an entity. Must be either a CURIE shorthand
      for a URI or a complete URI
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - AGRKB:primaryId
    - gff3:ID
    - gpi:DB_Object_ID
    rank: 1000
    domain: entity
    slot_uri: biolink:id
    identifier: true
    alias: id
    owner: DissociatedCellSample
    domain_of:
    - ontology class
    - entity
    - attribute
    - named thing
    - taxonomic rank
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    required: true
  iri:
    name: iri
    definition_uri: https://w3id.org/biolink/vocab/iri
    description: An IRI for an entity. This is determined by the id using expansion
      rules.
    in_subset:
    - translator_minimal
    - samples
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - WIKIDATA_PROPERTY:P854
    rank: 1000
    slot_uri: biolink:iri
    alias: iri
    owner: DissociatedCellSample
    domain_of:
    - attribute
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: iri type
  category:
    name: category
    definition_uri: https://w3id.org/biolink/vocab/category
    description: 'Name of the high level ontology class in which this entity is categorized.
      Corresponds to the label for the biolink entity type class. In a neo4j database
      this MAY correspond to the neo4j label tag. In an RDF database it should be
      a biolink model class URI. This field is multi-valued. It should include values
      for ancestors of the biolink class; for example, a protein such as Shh would
      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
      In an RDF database, nodes will typically have an rdf:type triples. This can
      be to the most specific biolink class, or potentially to a class more specific
      than something in biolink. For example, a sequence feature `f` may have a rdf:type
      assertion to a SO class such as TF_binding_site, which is more specific than
      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
      biolink:NamedThing}. NOTE: The category slot was modified to have a curie range
      and a pattern for bican categories.'
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    is_a: type
    domain: entity
    slot_uri: biolink:category
    designates_type: true
    alias: category
    owner: DissociatedCellSample
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    is_class_field: true
    range: curie
    multivalued: true
    pattern: ^bican:[A-Z][A-Za-z]+$
  type:
    name: type
    definition_uri: https://w3id.org/biolink/vocab/type
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    mappings:
    - rdf:type
    exact_mappings:
    - gff3:type
    - gpi:DB_Object_Type
    rank: 1000
    domain: entity
    slot_uri: rdf:type
    alias: type
    owner: DissociatedCellSample
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    multivalued: true
  description:
    name: description
    definition_uri: https://w3id.org/biolink/vocab/description
    description: a human-readable description of an entity
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    aliases:
    - definition
    mappings:
    - dct:description
    exact_mappings:
    - IAO:0000115
    - skos:definitions
    narrow_mappings:
    - gff3:Description
    rank: 1000
    slot_uri: dct:description
    alias: description
    owner: DissociatedCellSample
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: narrative text
  has attribute:
    name: has attribute
    definition_uri: https://w3id.org/biolink/vocab/has_attribute
    description: connects any entity to an attribute
    in_subset:
    - samples
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - SIO:000008
    close_mappings:
    - OBI:0001927
    narrow_mappings:
    - OBAN:association_has_subject_property
    - OBAN:association_has_object_property
    - CPT:has_possibly_included_panel_element
    - DRUGBANK:category
    - EFO:is_executed_in
    - HANCESTRO:0301
    - LOINC:has_action_guidance
    - LOINC:has_adjustment
    - LOINC:has_aggregation_view
    - LOINC:has_approach_guidance
    - LOINC:has_divisor
    - LOINC:has_exam
    - LOINC:has_method
    - LOINC:has_modality_subtype
    - LOINC:has_object_guidance
    - LOINC:has_scale
    - LOINC:has_suffix
    - LOINC:has_time_aspect
    - LOINC:has_time_modifier
    - LOINC:has_timing_of
    - NCIT:R88
    - NCIT:eo_disease_has_property_or_attribute
    - NCIT:has_data_element
    - NCIT:has_pharmaceutical_administration_method
    - NCIT:has_pharmaceutical_basic_dose_form
    - NCIT:has_pharmaceutical_intended_site
    - NCIT:has_pharmaceutical_release_characteristics
    - NCIT:has_pharmaceutical_state_of_matter
    - NCIT:has_pharmaceutical_transformation
    - NCIT:is_qualified_by
    - NCIT:qualifier_applies_to
    - NCIT:role_has_domain
    - NCIT:role_has_range
    - INO:0000154
    - HANCESTRO:0308
    - OMIM:has_inheritance_type
    - orphanet:C016
    - orphanet:C017
    - RO:0000053
    - RO:0000086
    - RO:0000087
    - SNOMED:has_access
    - SNOMED:has_clinical_course
    - SNOMED:has_count_of_base_of_active_ingredient
    - SNOMED:has_dose_form_administration_method
    - SNOMED:has_dose_form_release_characteristic
    - SNOMED:has_dose_form_transformation
    - SNOMED:has_finding_context
    - SNOMED:has_finding_informer
    - SNOMED:has_inherent_attribute
    - SNOMED:has_intent
    - SNOMED:has_interpretation
    - SNOMED:has_laterality
    - SNOMED:has_measurement_method
    - SNOMED:has_method
    - SNOMED:has_priority
    - SNOMED:has_procedure_context
    - SNOMED:has_process_duration
    - SNOMED:has_property
    - SNOMED:has_revision_status
    - SNOMED:has_scale_type
    - SNOMED:has_severity
    - SNOMED:has_specimen
    - SNOMED:has_state_of_matter
    - SNOMED:has_subject_relationship_context
    - SNOMED:has_surgical_approach
    - SNOMED:has_technique
    - SNOMED:has_temporal_context
    - SNOMED:has_time_aspect
    - SNOMED:has_units
    - UMLS:has_structural_class
    - UMLS:has_supported_concept_property
    - UMLS:has_supported_concept_relationship
    - UMLS:may_be_qualified_by
    rank: 1000
    domain: entity
    slot_uri: biolink:has_attribute
    alias: has_attribute
    owner: DissociatedCellSample
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: attribute
    multivalued: true
  deprecated:
    name: deprecated
    definition_uri: https://w3id.org/biolink/vocab/deprecated
    description: A boolean flag indicating that an entity is no longer considered
      current or valid.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - oboInOwl:ObsoleteClass
    rank: 1000
    slot_uri: biolink:deprecated
    alias: deprecated
    owner: DissociatedCellSample
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: boolean
  provided by:
    name: provided by
    definition_uri: https://w3id.org/biolink/vocab/provided_by
    description: The value in this node property represents the knowledge provider
      that created or assembled the node and all of its attributes.  Used internally
      to represent how a particular node made its way into a knowledge provider or
      graph.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:provided_by
    alias: provided_by
    owner: DissociatedCellSample
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    multivalued: true
  xref:
    name: xref
    definition_uri: https://w3id.org/biolink/vocab/xref
    description: A database cross reference or alternative identifier for a NamedThing
      or edge between two NamedThings.  This property should point to a database record
      or webpage that supports the existence of the edge, or gives more detail about
      the edge. This property can be used on a node or edge to provide multiple URIs
      or CURIE cross references.
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    aliases:
    - dbxref
    - Dbxref
    - DbXref
    - record_url
    - source_record_urls
    narrow_mappings:
    - gff3:Dbxref
    - gpi:DB_Xrefs
    rank: 1000
    domain: named thing
    slot_uri: biolink:xref
    alias: xref
    owner: DissociatedCellSample
    domain_of:
    - named thing
    - gene
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - genome
    range: uriorcurie
    multivalued: true
  full name:
    name: full name
    definition_uri: https://w3id.org/biolink/vocab/full_name
    description: a long-form human readable name for a thing
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:full_name
    alias: full_name
    owner: DissociatedCellSample
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: label type
  synonym:
    name: synonym
    definition_uri: https://w3id.org/biolink/vocab/synonym
    description: Alternate human-readable names for a thing
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    aliases:
    - alias
    narrow_mappings:
    - skos:altLabel
    - gff3:Alias
    - AGRKB:synonyms
    - gpi:DB_Object_Synonyms
    - HANCESTRO:0330
    - IAO:0000136
    - RXNORM:has_tradename
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:synonym
    alias: synonym
    owner: DissociatedCellSample
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: label type
    multivalued: true